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Now ID is the primary key of the table which means it has a unique index on it (right?)

that's correct, and as you can imagine, forcing uniqueness for a number that the database assigns sequentially might seem wasteful (it is), but the index is the important part of an auto_increment being a primary key

will adding the following have any additional effect?
CREATE index_name ON table(ID);

i'm not exactly sure, but i'm guessing the database will go ahead and create it (rather than tellin you "dude, what's the point, you already have an index on that column")

Or is such an index automatically created for all the primary keys in a table?

yes, except that there can only be one primary key

Also, putting storage issues aside, what would be the disadvantages to creating an index for every column that I use in a join, (in order to speed things up)?

the disadvantage is that while indexes speed up SELECTs, they slow down UPDATEs, DELETEs, and INSERTs